Spain are aiming to become the first side to win Olympic gold after lifting the Women's World Cup, having defeated England in the final of that tournament last year.
Ballon d'Or winner Bonmati levelled after Aoba Fujino's stunning 13th-minute free-kick opener in Nantes, before the Spain midfielder teed up Mariona Caldentey's winner 16 minutes from time.
That result saw Montserrat Tome's side seize top spot in Group C ahead of Brazil, who edged past Nigeria 1-0 thanks to Gabi Nunes' first-half finish.
Elsewhere in Group A, defending champions Canada put off-field issues to one side by overcoming New Zealand 2-1 thanks to goals from Cloe Lacasse and Evelyne Viens in Saint-Etienne.
Canada's integrity had been questioned ahead of the game in the wake of a spying scandal, with assistant Andy Spence serving as head coach after Bev Priestman volunteered to sit out.
Priestman, two members of her staff and the Canadian Olympic Committee are being investigated by FIFA's disciplinary committee after a drone was spotted flying over New Zealand's training on Monday.
"Obviously the timing was quite terrible," said Canada captain Jessie Fleming of the drone incident after her side battled back following Mackenzie Barry's early opener.
"But I think for us, we've just leaned into each other as a player group and we really just want to focus on being here and playing."
Hosts France seemed on course for a routine victory in the other Group A game after Marie-Antoinette Katoto's first-half double and Kadidiatou Diani's goal against Colombia.
However, Catalina Usme pulled one back from the spot and Manuela Pavi further reduced the deficit nine minutes later, only for Mayra Ramirez's late red card to help France hold out for a 3-2 victory.
Meanwhile, Germany swept aside Australia 3-0 in Group B, inflicting the Matildas' joint-heaviest defeat at the Olympics, along with a loss against the same opponent by the same scoreline, at Sydney 2000.
Efforts from Marina Hegering, Lea Schuller and Jule Brand sealed the victory for the DFB-Frauenteam against the Tokyo 2020 semi-finalists.
The defending Olympic champions had won both their group matches, but were docked six points after being found guilty of using a drone to spy on New Zealand's training session ahead of their opening match of the Games.
It subsequently saw head coach Bev Priestman banned from football-related activities for a year, and despite appealing the decision, saw it rejected.
However, Vanessa Gilles' header proved to be the difference as she rose highest to meet Jessie Fleming's corner kick delivery in the 61st minute.
While Canada only took three points from their group games, they joined both Spain and the United States as the only teams to win all their games at the tournament so far.
Colombia, who started the day's action in second, settled for third spot but advanced to the knockout stages as one of the best third-placed teams and will face Spain.
Canada, meanwhile, will continue their quest for a second Olympic triumph in the Parc des Princes on Saturday where they will face Germany.
In the other Group A fixture, hosts France confirmed their place in the knockout stages of the competition after a hard fought 2-1 triumph over New Zealand.
Marie-Antoinette Katoto scored the opening goal of the game in the 22nd minute, only for Kate Taylor to respond for the visitors two minutes before the interval.
Katoto, who scored a brace against Colombia in their opening group game, notched her second double of the tournament late on to take her tally to five at the Games and secure top spot for the French.
France will next be in action this Saturday in Nantes, where they will face Brazil, who will be without veteran striker Marta following her red card against Spain earlier in the day.
After being found guilty of using a drone to film opponents' training at this and past tournaments, the Tokyo champions had six points deducted, while head coach Bev Priestman has been banned from all football-related activity for one year.
The Canadian Soccer Association (CSA) are considering an appeal against the decision, but those controversies were put to one side when the team took to the field.
Starting the day bottom on -3 points, Canada, led by Andy Spence, had to come from behind to beat France after Marie-Antoinette Katoto put Les Bleues ahead just before half-time.
Jessie Fleming equalised from close range in the 58th minute, but Canada fought back, with Gilles getting some help from the woodwork to secure the win.
Meanwhile, Colombia's comfortable 2-0 victory over New Zealand means they now lead Group A after two games thanks to their goal difference.
Elsewhere, in Group C, Spain booked their place in the quarter-finals with a game to spare after a 1-0 win over Nigeria.
Alexia Putellas' long-range strike maintained La Roja's perfect start to the tournament as they bid to become the first team to win Olympic gold after lifting the Women's World Cup.
In the other group game, Japan ruined the party for Marta, who made her 200th appearance for Brazil in a shock 2-1 defeat.
Despite Mina Tanaka's penalty miss in the first half, Japan launched a comeback after Jheniffer's opener, with Saki Kumagai and Momoko Tanikawa both scoring in stoppage time to move second.
The game of the day came in Group B though, as Australia edged out Zambia in an 11-goal thriller.
Barbra Banda's hat-trick gave the minnows a 5-2 lead, but they could not hold onto it as Michelle Heyman made it 6-5 in the 90th minute to snatch a win.
Head coach Bev Priestman, who led Canada to their maiden gold medal success in Tokyo, has also voluntarily withdrawn from coaching her team’s Group A opener in Saint-Etienne on Thursday.
Fifa said it has opened disciplinary proceedings against Canada Soccer after New Zealand's women's team said their training session on Monday had been disrupted by a drone ahead of their encounter.
Jasmine Mander, Priestman's assistant, was sent home along with "unaccredited analyst" Joseph Lombardi following the incident.
Lombardi is the director of the National Development Centre Ontario and Women’s U-20 program. Mander was Priestman's assistant at the Tokyo Olympics in 2021 and the World Cup last summer.
Priestman apologised for what had happened and said the ultimate responsibility lay with her.
"I first and foremost want to apologise to the players and staff at New Zealand Football and to the players on Team Canada," Priestman said.
"This does not represent the values that our team stands for. I am ultimately responsible for conduct in our program."
The COC confirmed on Wednesday that a "non-accredited member of the Canada Soccer support team" was detained by authorities.
"The Canadian Olympic Committee stands for fair play and we are shocked and disappointed," it added in a statement.
"We offer our heartfelt apologies to New Zealand Football, to all the players affected, and to the New Zealand Olympic Committee."
